RetrogeneDB ID: retro_pabe_3228

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:10587126..10588328(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CTBP2
• Ensembl ID: ENSPPYG00000002746
• Aliases: None
• Description: C-terminal binding protein 2 [Source:HGNC Symbol;Acc:2495]

Sequence

>retro_pabe_3228
ATGACATTTGTGGATAAGCGCAAACTTAAGAGAGAGCGATTGGACAGAATTTGTGTAGGAATTCGCCTCCACATCATGAA
AGGCCCCCTGCACCCCCGCCCTGTGGTGGCGCTGCTGGACGGCCGCGACTGCATTGTGGACATGCCCATCCTGAAGGACC
TGGCCACCGTGGCCTTCTGTGATTTGCAGTCCACGCAGGAGATCCACGAGAAGGTTCTAAACAGAGTCGTGGGCGCCATG
ATATACAACACCATAACCCCCACCAGGGAGGACCTGGCAAATTTCAAGGACCTGAGAGTGATCGTGCGGGTTGGCAGTGG
CTACGACAACGTGAACATCAAGGCTGCTGGCGAGCTCGGAATTTCTGTGTGCAACATCCCGTCCGCAGCCGTGGAAGAGA
CAGCCTACTCCACTATCTGCCACATCCTCAACATGCACCAGAGGAACACATGGCTGTTCCAGGCACTGTGGGAAGGCAAG
CGGGTTCAGAGCGTGGAGTAGATCTGCGAGGCGGCCTCGGGAGTGGCCCCTATTCGTGGGGAGACGCTGGGCCTCATCGG
CTACAGTCGCACGCAGCAGGCTTTTGCGGTTCCAGCCACCGCCTTTGGATTCAGCGTCATATTTTATTACCCCTACTTGC
AGGATGGGATCGAGCTGTTCCTGGGAGTGCAGAGGGTCTACACACAGCAGGAATTGCTGTATCAGAGAGACTGCGTCTCC
TTGCACTGCAGTCTCAGCGAACATAAACACCACCTCATCAATGACTTTTCCAGAAAGCAGATGAGGTAGGGAGCATTCCT
TGTGAACACAGCCCGTTGTGGCCTGGTGGATGAGAAAGCCTTAGCACAGGCCCTCAAGGAGGGCAAGATACGAGGGGCAG
CCCTCGACGTGAATGAGTCATAGCCCTTTAGCTTGGCTCAGGGTCCATTGAAGATGTTCCGAATCTCATCTGCACTCCTC
ACACTGCCTGCTACAGCGAGCAGGCGTCACTGGAGATGAAAGAGGCAGCTGCCACCGAGATCCGCTGAACCATCACAGGT
CGCATCCCAGGAAGCTTAAGAAACTGTGTGAAAAAGCAATTCTTTGTCACATTTGTGCTTTGGTCAGTAATAGACCAGCA
AGCAATTCATCCAGTCATCGTGGGCGTGGCTCCAGGAGGACTTCCTGCATCCAATGAAGGGATCATCCCTGGATGCATCC
CG

Alignment

ORF - retro_pabe_3228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.11 %
• Parental protein coverage: 89.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALVDKHKVKRQRLDRICEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHE
          M..VDK.K.KR.RLDRIC.GIR..IM.GPLHPRP.VALLDGRDC.V.MPILKDLATVAFCD.QSTQEIHE
Retrocopy MTFVDKRKLKRERLDRICVGIRLHIMKGPLHPRPVVALLDGRDCIVDMPILKDLATVAFCDLQSTQEIHE

Parental  KVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTIC
          KVLN..VGAM.Y.TIT.TREDL..FK.LRVIVR.GSGYDNV.IKAAGELGI.VCNIPSAAVEETA.STIC
Retrocopy KVLNRVVGAMIYNTITPTREDLANFKDLRVIVRVGSGYDNVNIKAAGELGISVCNIPSAAVEETAYSTIC

Parental  HILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYD
          HILN...RNTWL.QAL.EG.RVQSVE.I.E.ASG.A.IRGETLGLIG..RT.QA.AV.A.AFGFSVIFY.
Retrocopy HILNMHQRNTWLFQALWEGKRVQSVE*ICEAASGVAPIRGETLGLIGYSRTQQAFAVPATAFGFSVIFYY

Parental  PYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKA
          PYLQDGIE..LGVQRVYT.Q.LLYQ.DCVSLHC.L.EH.HHLINDF..KQMR.GAFLVN.AR.GLVDEKA
Retrocopy PYLQDGIELFLGVQRVYTQQELLYQRDCVSLHCSLSEHKHHLINDFSRKQMR*GAFLVNTARCGLVDEKA

Parental  LAQALKEGRIRGAALDVHESEPFSFAQGPLK-DAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRI
          LAQALKEG.IRGAALDV.ES.PFS.AQGPLK.D.PNLICTPHTA.YSEQASLEM.EAAATEIR..ITGRI
Retrocopy LAQALKEGKIRGAALDVNES*PFSLAQGPLK<DVPNLICTPHTACYSEQASLEMKEAAATEIR*TITGRI

Parental  PESLRNCVNKEFFVTSAPWSVIDQQAIHPELNG-ATYRYPPGIVGVAPGGLP
          P.SLRNCV.K.FFVT...WSVIDQQAIHP...G.A....P....G..PG..P
Retrocopy PGSLRNCVKKQFFVTFVLWSVIDQQAIHPVIVGVAPGGLPASNEGIIPGCIP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.96 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	3.97 RPM
SRP007412_kidney	0.00 RPM	15.51 RPM
SRP007412_liver	0.00 RPM	2.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3228 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3228 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012775	1 retrocopy	retro_cfam_1868,
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528,
Homo sapiens	ENSG00000175029	1 retrocopy	retro_hsap_403,
Oryctolagus cuniculus	ENSOCUG00000007076	1 retrocopy	retro_ocun_378,
Pongo abelii	ENSPPYG00000002746	10 retrocopies	retro_pabe_1706, retro_pabe_1710, retro_pabe_1711, retro_pabe_1719, retro_pabe_1737, retro_pabe_1750, retro_pabe_1773, retro_pabe_3228 , retro_pabe_3230, retro_pabe_3587,